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Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
PhyloSort sorts phylogenetic trees by searching for user-specified subtrees that contain a monophyletic group of interest defined by operational taxonomic units.
HATS (Haplotype Amplification in Tumor Sequences) is a tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data. The amplified haplotype may reveal gene variants.
Enrich and query corpora in the TEI-XML vocabulary. CorpusReader manage very large corpora and corpora containing milestone annotation. It provides tools for enriching corpora with output of linguistic parsers, and for extracting quantitative information
A program to calculate and create lists of possible variations (permutations) and selections (combinations) of a given set of elements. Creating the cartesian product of two sets is also possible.
Cougar Squared is a new Java library for machine learning and data mining research, supporting research needs of the community. It is written by researchers for researchers. It extends the WEKA and YALE machine learning frameworks.
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Volta is a suite of development tools for distributed, hard real-time systems. It includes Cascade, a control flow analysis tool for Java, and Clepsydra, a worst-case execution time analyzer. Also included is a Clepsydra plug-in for jEdit.
GISpatialNet is a Java-based tool for mapping network data (nodes and edges between them) to spatial coordinates; reformatting network and spatial data together; and calculating spatial network measures.
Install by saving to c:\ drive and typing the following in a command line:
java -jar c:\GISpatialNet-0.9b.jar
RoboBeans is an interface to the "Robocup 2D Soccer Simulation Server" that allows developers to write Robocup teams\agents concentrating on behaviour and AI without having to worry about syntax of communication or network issues.
haggies is an optimizing code generator. It can read in expressions in common notation and generate output for many programming languages including C/C++, Java, Fortran, Python and many others.
This is a MATLAB toolbox for the quality control and scoring of EMAP and SGA genetic interaction data. It includes a graphical user interface and some automatic plot-generating tools.
A Java package that provides several computations related to the edit distance of strings. Other than the basic Levenshtein, this algorithm can rearange words when comparing. The class can also provide details of how words could be transformed.
Data mining tool for sequences (e.g. trajectories on a map, visited web pages, etc.) that creates a succinct description of the sequences, given a taxonomy (e.g. regions and sub-regions in the map, categories and sub-categories of pages, etc.).
OSM XML to CSV conversion. POI only, polygons (and polylines, but not recommended) are approximated by centroid. Result is a 3-column table with lon, lat and value (for a particular key to be chosen beforehand).
Mostly academic research Project about next generation computing (Software only), trying to find new ideas and solutions how computers can work in the future using technologies like voice recognition and synthesisation. Everyone is invited to join in
JTHERGAS (a JAVA implementation of THERGAS) estimates thermodynamic information from two dimensional graphical representations of molecules and radicals based on the Benson additivity method.
GridSim allows modeling and simulation of entities in parallel and distributed computing systems such as users, applications, resources, and resource brokers/schedulers for design and evaluation of scheduling algorithms. http://www.gridbus.org/gridsim